Consolidated encounters into a single NetCDF file

python/swiftest/swiftest/simulation_class.py

@@ -2753,22 +2753,13 @@ def read_output_file(self,read_init_cond : bool = True):
         return
 
     def read_encounter(self):
-        enc_files = glob(f"{self.simdir}{os.path.sep}encounter_*.nc")
-        if len(enc_files) == 0:
-            return
-
-        if self.verbose:
-            print("Reading encounter history file as .encounters")
-
-        enc_files.sort()
+        enc_file = self.simdir / "encounters.nc"
+        if not os.path.exists(enc_file):
+           return
 
-        # This is needed in order to pass the param argument down to the io.process_netcdf_input function
-        def _preprocess(ds, param):
-            return io.process_netcdf_input(ds,param)
-        partial_func = partial(_preprocess, param=self.param)
+        self.collisions = xr.open_dataset(enc_file)
+        self.collisions = io.process_netcdf_input(self.collisions, self.param)
 
-        self.encounters = xr.open_mfdataset(enc_files,parallel=True,combine="nested",concat_dim="time",join="left",preprocess=partial_func,mask_and_scale=True)
-        self.encounters = io.process_netcdf_input(self.encounters, self.param)
         # Remove any overlapping time values
         tgood,tid = np.unique(self.encounters.time,return_index=True)
         self.encounters = self.encounters.isel(time=tid)

src/collision/collision_module.f90

@@ -18,8 +18,8 @@ module collision
    implicit none
    public
 
-   character(len=*), parameter :: COLLISION_OUTFILE = 'collision.nc'  !! Name of NetCDF output file for collision information
-   character(len=*), parameter :: COLLISION_LOG_OUT = "collision.log" !! Name of log file for collision diagnostic information
+   character(len=*), parameter :: COLLISION_OUTFILE = 'collisions.nc'  !! Name of NetCDF output file for collision information
+   character(len=*), parameter :: COLLISION_LOG_OUT = "collisions.log" !! Name of log file for collision diagnostic information
 
    !>Symbolic names for collisional outcomes from collresolve_resolve:
    integer(I4B), parameter :: COLLRESOLVE_REGIME_MERGE              =  1

src/encounter/encounter_io.f90

@@ -26,13 +26,8 @@ module subroutine encounter_io_netcdf_dump(self, param)
       class is (encounter_netcdf_parameters)
          if (self%iframe > 0) then
             ! Create and save the output files for this encounter and fragmentation
-            nc%file_number = nc%file_number + 1 
             call self%make_index_map()
-            nc%time_dimsize = self%nt
-            nc%name_dimsize = self%nid
-            write(nc%file_name, '("encounter_",I0.6,".nc")') nc%file_number
-            call nc%initialize(param)
-
+            call nc%open(param)
             do i = 1, self%iframe
                if (allocated(self%frame(i)%item)) then
                   select type(snapshot => self%frame(i)%item)
@@ -153,6 +148,75 @@ module subroutine encounter_io_netcdf_initialize_output(self, param)
    end subroutine encounter_io_netcdf_initialize_output
 
 
+   module subroutine encounter_io_netcdf_open(self, param, readonly)
+      !! author: Carlisle A. Wishard, Dana Singh, and David A. Minton
+      !!
+      !! Opens a NetCDF file and does the variable inquiries to activate variable ids
+      use netcdf
+      implicit none
+      ! Arguments
+      class(encounter_netcdf_parameters), intent(inout) :: self     !! Parameters used to identify a particular NetCDF dataset
+      class(base_parameters),             intent(in)    :: param    !! Current run configuration parameters
+      logical, optional,                  intent(in)    :: readonly !! Logical flag indicating that this should be open read only
+      ! Internals
+      integer(I4B) :: mode
+      character(len=STRMAX) :: errmsg
+      logical fileExists
+
+      mode = NF90_WRITE
+      if (present(readonly)) then
+         if (readonly) mode = NF90_NOWRITE
+      end if
+
+      select type(param)
+      class is (base_parameters)
+         associate(nc => self)
+
+            inquire(file=nc%file_name, exist=fileExists)
+            if (.not.fileExists) then
+               call nc%initialize(param)
+               return
+            end if
+
+            write(errmsg,*) "encounter_io_netcdf_opennf90_open ",trim(adjustl(nc%file_name))
+            call netcdf_io_check( nf90_open(nc%file_name, mode, nc%id), errmsg)
+            self%lfile_is_open = .true.
+
+            ! Dimensions
+            call netcdf_io_check( nf90_inq_dimid(nc%id, nc%time_dimname, nc%time_dimid), "encounter_io_netcdf_opennf90_inq_dimid time_dimid"  )
+            call netcdf_io_check( nf90_inq_dimid(nc%id, nc%space_dimname, nc%space_dimid), "encounter_io_netcdf_opennf90_inq_dimid space_dimid"  )
+            call netcdf_io_check( nf90_inq_dimid(nc%id, nc%name_dimname, nc%name_dimid), "encounter_io_netcdf_opennf90_inq_dimid name_dimid"  )
+            call netcdf_io_check( nf90_inq_dimid(nc%id, nc%str_dimname, nc%str_dimid), "encounter_io_netcdf_opennf90_inq_dimid str_dimid"  )
+
+            ! Dimension coordinates
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%time_dimname, nc%time_varid), "encounter_io_netcdf_opennf90_inq_varid time_varid" )
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%space_dimname, nc%space_varid), "encounter_io_netcdf_opennf90_inq_varid space_varid" )
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%name_dimname, nc%name_varid), "encounter_io_netcdf_opennf90_inq_varid name_varid" )
+
+            ! Required Variables
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%id_varname, nc%id_varid), "encounter_io_netcdf_opennf90_inq_varid name_varid" )
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%ptype_varname, nc%ptype_varid), "encounter_io_netcdf_opennf90_inq_varid ptype_varid" )
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%time_dimname, nc%time_varid), "encounter_io_netcdf_opennf90_inq_varid time_varid" )
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%rh_varname, nc%rh_varid), "encounter_io_netcdf_opennf90_inq_varid rh_varid" )
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%vh_varname, nc%vh_varid), "encounter_io_netcdf_opennf90_inq_varid vh_varid" )
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%Gmass_varname, nc%Gmass_varid), "encounter_io_netcdf_opennf90_inq_varid Gmass_varid" )
+            call netcdf_io_check( nf90_inq_varid(nc%id, nc%loop_varname, nc%loop_varid), "encounter_io_netcdf_opennf90_inq_varid loop_varid" )
+            if (param%lclose) then
+               call netcdf_io_check( nf90_inq_varid(nc%id, nc%radius_varname, nc%radius_varid), "encounter_io_netcdf_opennf90_inq_varid radius_varid" )
+            end if
+
+            if (param%lrotation) then
+               call netcdf_io_check( nf90_inq_varid(nc%id, nc%Ip_varname, nc%Ip_varid), "encounter_io_netcdf_opennf90_inq_varid Ip_varid" )
+               call netcdf_io_check( nf90_inq_varid(nc%id, nc%rot_varname, nc%rot_varid), "encounter_io_netcdf_opennf90_inq_varid rot_varid" )
+            end if
+
+         end associate
+      end select 
+
+      return
+   end subroutine encounter_io_netcdf_open
+
+
    module subroutine encounter_io_netcdf_write_frame_snapshot(self, history, param)
       !! author: David A. Minton
       !!

src/encounter/encounter_module.f90

@@ -18,6 +18,7 @@ module encounter
    public
 
    integer(I4B), parameter :: SWEEPDIM = 3
+   character(len=*), parameter :: ENCOUNTER_OUTFILE = 'encounters.nc'  !! Name of NetCDF output file for encounter information
 
    type, abstract :: encounter_list
       integer(I8B)                              :: nenc = 0   !! Total number of encounters
@@ -67,6 +68,7 @@ module encounter
       integer(I4B)       :: file_number  = 1         !! The number to append on the output file
    contains
       procedure :: initialize => encounter_io_netcdf_initialize_output !! Initialize a set of parameters used to identify a NetCDF output object
+      procedure :: open       => encounter_io_netcdf_open              !! Open an encounter NetCDF file
       final     ::               encounter_final_netcdf_parameters     !! Finalizer will close the NetCDF file
    end type encounter_netcdf_parameters
 
@@ -229,6 +231,13 @@ module subroutine encounter_io_netcdf_initialize_output(self, param)
          class(base_parameters),     intent(in)    :: param   
       end subroutine encounter_io_netcdf_initialize_output
 
+      module subroutine encounter_io_netcdf_open(self, param, readonly)
+         implicit none
+         class(encounter_netcdf_parameters), intent(inout) :: self     !! Parameters used to identify a particular NetCDF dataset
+         class(base_parameters),             intent(in)    :: param    !! Current run configuration parameters
+         logical, optional,                  intent(in)    :: readonly !! Logical flag indicating that this should be open read only
+      end subroutine encounter_io_netcdf_open
+
       module subroutine encounter_io_netcdf_write_frame_snapshot(self, history, param)
          implicit none
          class(encounter_snapshot),   intent(in)    :: self    !! Swiftest encounter structure
@@ -272,7 +281,6 @@ module subroutine encounter_util_dealloc_list(self)
          class(encounter_list), intent(inout) :: self !! Swiftest encounter list object
       end subroutine encounter_util_dealloc_list
 
-
       module subroutine encounter_util_get_idvalues_snapshot(self, idvals)
          implicit none
          class(encounter_snapshot),               intent(in)  :: self   !! Encounter snapshot object

src/swiftest/swiftest_util.f90

@@ -2608,7 +2608,11 @@ module subroutine swiftest_util_setup_construct_system(nbody_system, param)
                call encounter_history%reset()
                select type(nc => encounter_history%nc)
                class is (encounter_netcdf_parameters)
-                  nc%file_number = param%iloop / param%dump_cadence
+                  nc%file_name = ENCOUNTER_OUTFILE
+                  if (.not.param%lrestart) then
+                     call nc%initialize(param)
+                     call nc%close()
+                  end if
                end select
                allocate(nbody_system%encounter_history, source=encounter_history)
             end if